/// <summary>
/// Get a smoothed XIC.
/// </summary>
/// <param name="smoother">Smoother to smooth XIC.</param>
/// <param name="xic">XIC to smooth.</param>
/// <returns>Array of smoothed XIC points.</returns>
public static XicPoint[] SmoothXic(SavitzkyGolaySmoother smoother, IList <XicPoint> xic)
{
var xicP = new double[xic.Count];
for (var i = 0; i < xic.Count; i++)
{
xicP[i] = xic[i].Intensity;
}
double[] smoothedPoints;
try
{
smoothedPoints = smoother.Smooth(xicP);
}
catch (IndexOutOfRangeException)
{
smoothedPoints = xicP;
}
var smoothedXic = new XicPoint[xicP.Length];
for (var i = 0; i < xicP.Length; i++)
{
smoothedXic[i] = new XicPoint(xic[i].ScanNum, xic[i].Mz, smoothedPoints[i]);
}
return(smoothedXic);
}
/// <summary>
/// Smooth and snip tails off a single XIC.
/// </summary>
/// <param name="xic">The XIC to refine.</param>
/// <returns>Refined XIC.</returns>
public Xic RefineXic(Xic xic)
{
// Here we smooth the points...and remove any features with from and trailing zero points
if (xic.Count == 0)
{
return(xic);
}
var unsmoothedPoints = xic.Select(xicp => new XYData(xicp.ScanNum, xicp.Intensity))
.OrderBy(p => p.X).ToList();
var points = smoother.Smooth(unsmoothedPoints);
// Find the biggest peak...
var maxScanIndex = 0;
double maxAbundance = 0;
for (var i = 0; i < xic.Count; i++)
{
if (maxAbundance < xic[i].Intensity)
{
maxScanIndex = i;
maxAbundance = xic[i].Intensity;
}
}
// Then find when the feature goes to zero
// Start from max to left
var startIndex = maxScanIndex;
// If we hit zero, then keep
for (; startIndex > 0; startIndex--)
{
if ((xic[startIndex].Intensity / maxAbundance) < this.relativeIntensityThreshold)
{
break;
}
}
// Start from max to right
var stopIndex = maxScanIndex;
for (; stopIndex < xic.Count - 1; stopIndex++)
{
if ((xic[stopIndex].Intensity / maxAbundance) < this.relativeIntensityThreshold)
{
break;
}
}
// Add the features back
for (var i = startIndex; i <= stopIndex; i++)
{
xic[i] = new XicPoint(Convert.ToInt32(xic[i].ScanNum), xic[i].Mz, Convert.ToInt64(points[i].Y));
}
return(xic);
}
public new Xic GetFullProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz)
{
var xic = GetProductExtractedIonChromatogram(minMz, maxMz, precursorIonMz);
var scanToXicPoint = new XicPoint[MaxLcScan - MinLcScan + 1];
foreach (var xicPoint in xic) scanToXicPoint[xicPoint.ScanNum - MinLcScan] = xicPoint;
var newXic = new Xic();
newXic.AddRange(GetFragmentationSpectraScanNums(precursorIonMz).Select(scanNum => scanToXicPoint[scanNum - MinLcScan] ?? new XicPoint(scanNum, 0, 0)));
return newXic;
}
public new Xic GetFullProductExtractedIonChromatogram(double minMz, double maxMz, double precursorIonMz)
{
var xic = GetProductExtractedIonChromatogram(minMz, maxMz, precursorIonMz);
var scanToXicPoint = new XicPoint[MaxLcScan - MinLcScan + 1];
foreach (var xicPoint in xic)
{
scanToXicPoint[xicPoint.ScanNum - MinLcScan] = xicPoint;
}
var newXic = new Xic();
newXic.AddRange(GetFragmentationSpectraScanNums(precursorIonMz).Select(scanNum => scanToXicPoint[scanNum - MinLcScan] ?? new XicPoint(scanNum, 0, 0)));
return(newXic);
}